@Override
protected void setOptionFromMapEntry(ConanParameter param, String value) {
Params params = this.getParams();
if (param.equals(params.getGenomeDir())) {
this.genomeDir = new File(value);
} else if (param.equals(params.getGenomeDB())) {
this.genomeDB = value;
} else if (param.equals(params.getNovelSplicing())) {
this.novelSplicing = Integer.parseInt(value) > 0;
} else if (param.equals(params.getLocalSplicedDist())) {
this.localSplicedDist = Integer.parseInt(value);
} else if (param.equals(params.getThreads())) {
this.threads = Integer.parseInt(value);
} else if (param.equals(params.getOutputFormat())) {
this.outputFormat = value;
} else if (param.equals(params.getNbPaths())) {
this.nbPaths = Integer.parseInt(value);
} else if (param.equals(params.getBatch())) {
this.batch = Integer.parseInt(value);
} else if (param.equals(params.getExpandOffsets())) {
this.expandOffsets = value.equalsIgnoreCase("1") ? true : false;
} else if (param.equals(params.getKmer())) {
this.kmer = Integer.parseInt(value);
} else {
throw new IllegalArgumentException("Unknown param found: " + param);
}
}
@Override
protected void setOptionFromMapEntry(ConanParameter param, String value) {
Params params = this.getParams();
if (param.equals(params.getJobPrefix())) {
this.jobPrefix = value;
} else if (param.equals(params.getRunParallel())) {
this.runParallel = Boolean.parseBoolean(value);
} else {
throw new IllegalArgumentException("Unknown param found: " + param);
}
}
@Override
protected void setArgFromMapEntry(ConanParameter param, String value) {
Params params = this.getParams();
if (param.equals(params.getRead1())) {
this.read1 = new File(value);
} else if (param.equals(params.getRead2())) {
this.read2 = new File(value);
} else {
throw new IllegalArgumentException("Unknown param found: " + param);
}
}
@Override
protected void setStdErrRedirectFromMapEntry(ConanParameter param, String value) {
Params params = this.getParams();
if (param.equals(params.getLogFile())) {
this.logFile = new File(value);
} else {
throw new IllegalArgumentException("Unknown param found: " + param);
}
}